Its colonel was James's illegitimate son Henry Fitzjames, Grand Prior of the Knights of Malta, although in practice field command was delegated to an experienced lieutenant-colonel.

The Grand Prior's Regiment had its origin in the huge expansion of the Irish Army authorised by the Lord Deputy, the Earl of Tyrconnell, in the months following the deposition of James in the Glorious Revolution.

[5] While most of the Irish Jacobite regiments were poorly documented, the movements of the Grand Prior's are known in some detail thanks to the diary of John Stevens, an English Catholic who fled to France after James's deposition.

[6] At the Battle of the Boyne in July 1690, Stevens recorded that the appearance of the routed Jacobite cavalry caused the Grand Prior's to "[take] to their heels [...] I wondered what madness possessed our men to run so violently nobody pursuing them".

[7] The regiment gradually reassembled at Limerick; Stevens noted that without having even made contact with the enemy it had been reduced from 800 to 300 men, of whom only half had weapons, and its officers' baggage had been plundered twice by members of their own army.

[12] The Jacobite army was in an extremely poor state on arrival in France and was completely reorganised on terms largely dictated by the French, despite James's attempts to preserve its autonomy.

[15] Under the terms of the 1697 Peace of Ryswick which concluded the war, the Grand Prior's was one of the few regiments to survive the disbandment of most of James's army in exile.